pal.datatype
Class SimpleDataType

java.lang.Object
  pal.datatype.SimpleDataType

All Implemented Interfaces:

java.io.Serializable, DataType

Direct Known Subclasses:

AminoAcids, Codons, GapBalanced, IUPACNucleotides, Nucleotides, NumericDataType, StateRemover, TwoStates

public abstract class SimpleDataType
extends java.lang.Object
implements DataType

interface for sequence data types

Version:

$Id: SimpleDataType.java,v 1.14 2003/11/30 05:29:22 matt Exp $

Author:

Alexei Drummond

See Also:

Serialized Form

Nested Class Summary

Nested classes/interfaces inherited from interface pal.datatype.DataType

DataType.Utils

Field Summary

Fields inherited from interface pal.datatype.DataType

AMINO_ACID_DESCRIPTION, AMINOACIDS, CODON_DESCRIPTION, CODONS, GAP_BALANCED, GAP_BALANCED_DESCRIPTION, IUPAC_NUCELOTIDES_DESCRIPTION, IUPACNUCLEOTIDES, NUCLEOTIDE_DESCRIPTION, NUCLEOTIDES, NUMERIC, PRIMARY_SUGGESTED_GAP_CHARACTER, SUGGESTED_GAP_CHARACTERS, SUGGESTED_GAP_STATE, SUGGESTED_UNKNOWN_STATE, TWO_STATE_DESCRIPTION, TWOSTATES, UNKNOWN, UNKNOWN_CHARACTER, UNKNOWN_TLA

Constructor Summary

SimpleDataType()

Method Summary

AmbiguousDataType	getAmbiguousVersion()
char	getChar(int state) Handles gap state and then passes on to getStateImpl
protected abstract char	getCharImpl(int state)
char	getPreferredChar(char c) Automatically handles Gaps for sub classes
protected char	getPreferredCharImpl(char c) Can be overidden by subclasses.
int	getRecommendedGapState()
int	getRecommendedUnknownState()
int	getState(char c) Handles gap char and then passes on to getStateImpl
protected abstract int	getStateImpl(char c) For sub classes to implement main functionality of getState.
boolean	hasGap()
boolean	isAmbiguous()
boolean	isGapChar(char c)
boolean	isGapState(int state)
boolean	isUnknownChar(char c)
boolean	isUnknownState(int state) Checks if state is a gap state (then returns true), otherwise passes on to isUnknownStateImpl
protected abstract boolean	isUnknownStateImpl(int state) For subclasses to handle, without regard for gaps
java.lang.String	toString()

Methods inherited from class java.lang.Object

clone, equals, finalize, getClass, hashCode, notify, notifyAll, wait, wait, wait

Methods inherited from interface pal.datatype.DataType

getDescription, getNumStates, getTypeID

Constructor Detail

SimpleDataType

public SimpleDataType()

Method Detail

getState

public final int getState(char c)

Handles gap char and then passes on to getStateImpl

Specified by:

getState in interface DataType

Parameters:

c - character

Returns:

state

getChar

public final char getChar(int state)

Handles gap state and then passes on to getStateImpl

Specified by:

getChar in interface DataType

Parameters:

state - state return corresponding character

getStateImpl

protected abstract int getStateImpl(char c)

For sub classes to implement main functionality of getState. Gaps do not need to be considered

getCharImpl

protected abstract char getCharImpl(int state)

getPreferredChar

public final char getPreferredChar(char c)

Automatically handles Gaps for sub classes

Specified by:

getPreferredChar in interface DataType

getPreferredCharImpl

protected char getPreferredCharImpl(char c)

Can be overidden by subclasses. Default implementation get's character's state and that get's the character for that state

isUnknownChar

public final boolean isUnknownChar(char c)

Specified by:

isUnknownChar in interface DataType

Returns:

true if this state is unknown (or a gap)

isUnknownState

public final boolean isUnknownState(int state)

Checks if state is a gap state (then returns true), otherwise passes on to isUnknownStateImpl

Specified by:

isUnknownState in interface DataType

Returns:

true if this state is an unknown state (the same as check if a state is >= the number of states... but neater)

isUnknownStateImpl

protected abstract boolean isUnknownStateImpl(int state)

For subclasses to handle, without regard for gaps

toString

public java.lang.String toString()

Overrides:

toString in class java.lang.Object

getRecommendedUnknownState

public int getRecommendedUnknownState()

Specified by:

getRecommendedUnknownState in interface DataType

Returns:

-1 (not getNumStates())

isAmbiguous

public boolean isAmbiguous()

Specified by:

isAmbiguous in interface DataType

Returns:

false

getAmbiguousVersion

public AmbiguousDataType getAmbiguousVersion()

Specified by:

getAmbiguousVersion in interface DataType

Returns:

null

hasGap

public final boolean hasGap()

Specified by:

hasGap in interface DataType

Returns:

true

isGapChar

public final boolean isGapChar(char c)

Specified by:

isGapChar in interface DataType

Returns:

true if this character is a '.' or a '_'

isGapState

public final boolean isGapState(int state)

Specified by:

isGapState in interface DataType

Returns:

true if state is gap state (-2), false other wise

getRecommendedGapState

public final int getRecommendedGapState()

Specified by:

getRecommendedGapState in interface DataType

Returns:

GAP_STATE (-2)